Tukey HSD (or other post hoc tests) following repeated measures ANOVA

6 messages
Open this post in threaded view
|
Report Content as Inappropriate

Tukey HSD (or other post hoc tests) following repeated measures ANOVA

 Hi everyone, I am fairly new to R, and I am aware that others have had this problem before, but I have failed to solve the problem from previous replies I found in the archives. As this is such a standard procedure in psychological science, there must be an elegant solution to this...I think. I would much appreciate a solution that even I could understand... ;-) Now, I want to calculate a post-hoc test following up a within-subjects ANOVA. The dv is reaction time (RT), there is a 3-level Condition factor (Cond; within-subjects), a number of subjects (Subj), and the dataframe is called WMU3C. The model is  > RT.aov <- aov(RT~Cond + Error(Subj/Cond), WMU3C) I understand that TukeyHSD only works with an aov object, but that RT.aov is an aovlist object.  > class(RT.aov) [1] "aovlist" "listof" I've tried to work around it using the "maiz" example in the MMC documentation of the HH package (a solution previously recommended), but I couldn't get it to work: My best shot was to calculate another aov avoiding the error term (I don't see how this could be a feasible approach, but that's how I understood the MMC example) and a contrast vector (contrasting conditions 2 and 3): I have to admit that I don't quite understand what I'm doing here (not that you couldn't tell)  > RT2.aov <- aov(terms(RT~Subj*Cond, WMU3C))  > Cond.lmat <- c(0,1,-1)  > Tukey <- glht.mmc(RT2.aov, focus = "Cond", focus.lmat = Cond.lmat) yielding Error in mvt(lower = carg\$lower, upper = carg\$upper, df = df, corr = carg\$corr,  :    NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In cov2cor(covm) : diagonal has non-finite entries  > Tukey        height Thank you very much for your help! Ullrich Dr Ullrich Ecker Postdoctoral Research Associate Cognitive Science Laboratories School of Psychology (Mailbag M304) Room 211 Sanders Building University of Western Australia 35 Stirling Hwy Crawley WA 6009 Australia Office: +61 8 6488 3266 Mobile: +61 4 5822 0072 Fax: +61 8 6488 1006 E-mail: [hidden email] Web: www.cogsciwa.com           [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
Open this post in threaded view
|
Report Content as Inappropriate

Re: Tukey HSD (or other post hoc tests) following repeated measures ANOVA

 Ullrich Ecker uwa.edu.au> writes: > I am fairly new to R, and I am aware that others have had this > problem before, but I have failed to solve the problem from previous > replies I found in the archives. > > Now, I want to calculate a post-hoc test following up a within-subjects ANOVA. Probably the best is package multcomp. By default, it gives confidence intervals, which is certainly much better than p-values. Haven't tried if you can get p-values. Dieter library(multcomp) amod <- aov(breaks ~ wool + tension, data = warpbreaks) wht <- glht(amod, linfct = mcp(tension = "Tukey")) ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
Open this post in threaded view
|
Report Content as Inappropriate

Re: Tukey HSD (or other post hoc tests) following repeated measures ANOVA

 Thanks, Dieter, but as far as I understand,  'glht' does not support objects of class 'aovlist' either. I mean, I know there is a "TukeyHSD" function out there, but that's the problem: repeated measures ANOVA yields an aovlist object, and TukeyHSD calls for an aov object. And I don't know if confidence intervals are "certainly much better than p-values". What I do know is that most journals of psychology (and medicine, neuroscience, ...for that matter) usually require p-values be reported. Still hope someone can help... Ullrich At 06:31 PM 28/05/2008, you wrote: >Ullrich Ecker uwa.edu.au> writes: > > > I am fairly new to R, and I am aware that others have had this > > problem before, but I have failed to solve the problem from previous > > replies I found in the archives. > > > > Now, I want to calculate a post-hoc test following up a > within-subjects ANOVA. > > >Probably the best is package multcomp. By default, it gives confidence >intervals, which is certainly much better than p-values. Haven't tried if you >can get p-values. > >Dieter > > >library(multcomp) >amod <- aov(breaks ~ wool + tension, data = warpbreaks) >wht <- glht(amod, linfct = mcp(tension = "Tukey")) > >______________________________________________ >[hidden email] mailing list >https://stat.ethz.ch/mailman/listinfo/r-help>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html>and provide commented, minimal, self-contained, reproducible code. ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
Open this post in threaded view
|
Report Content as Inappropriate

Re: Tukey HSD (or other post hoc tests) following repeated measures ANOVA

 In reply to this post by Ullrich Ecker Hi Ullrich, >> The model is >> RT.aov <- aov(RT~Cond + Error(Subj/Cond), WMU3C) >> I understand that TukeyHSD only works with an aov object, but that >> RT.aov is an aovlist object. You want to use lme() in package nlme, then glht() in the multcomp package.  This will give you multiplicity adjusted p-values and confidence intervals. ## Example require(MASS)         ## for oats data set require(nlme)         ## for lme() require(multcomp)  ## for multiple comparison stuff Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats) Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats) summary(Aov.mod) anova(Lme.mod) summary(Lme.mod) summary(glht(Lme.mod, linfct=mcp(V="Tukey"))) HTH, Mark. Ullrich Ecker wrote Hi everyone, I am fairly new to R, and I am aware that others have had this problem before, but I have failed to solve the problem from previous replies I found in the archives. As this is such a standard procedure in psychological science, there must be an elegant solution to this...I think. I would much appreciate a solution that even I could understand... ;-) Now, I want to calculate a post-hoc test following up a within-subjects ANOVA. The dv is reaction time (RT), there is a 3-level Condition factor (Cond; within-subjects), a number of subjects (Subj), and the dataframe is called WMU3C. The model is  > RT.aov <- aov(RT~Cond + Error(Subj/Cond), WMU3C) I understand that TukeyHSD only works with an aov object, but that RT.aov is an aovlist object.  > class(RT.aov) [1] "aovlist" "listof" I've tried to work around it using the "maiz" example in the MMC documentation of the HH package (a solution previously recommended), but I couldn't get it to work: My best shot was to calculate another aov avoiding the error term (I don't see how this could be a feasible approach, but that's how I understood the MMC example) and a contrast vector (contrasting conditions 2 and 3): I have to admit that I don't quite understand what I'm doing here (not that you couldn't tell)  > RT2.aov <- aov(terms(RT~Subj*Cond, WMU3C))  > Cond.lmat <- c(0,1,-1)  > Tukey <- glht.mmc(RT2.aov, focus = "Cond", focus.lmat = Cond.lmat) yielding Error in mvt(lower = carg\$lower, upper = carg\$upper, df = df, corr = carg\$corr,  :    NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In cov2cor(covm) : diagonal has non-finite entries  > Tukey        height Thank you very much for your help! Ullrich Dr Ullrich Ecker Postdoctoral Research Associate Cognitive Science Laboratories School of Psychology (Mailbag M304) Room 211 Sanders Building University of Western Australia 35 Stirling Hwy Crawley WA 6009 Australia Office: +61 8 6488 3266 Mobile: +61 4 5822 0072 Fax: +61 8 6488 1006 E-mail: ullrich.ecker@uwa.edu.au Web: www.cogsciwa.com           [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa
Open this post in threaded view
|
Report Content as Inappropriate